[2024-01-24 14:50:03,445] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:50:03,447] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:50:03,447] [INFO] DQC Reference Directory: /var/lib/cwl/stg5343bc1a-74c8-4481-971c-c0df48e5432d/dqc_reference
[2024-01-24 14:50:04,849] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:50:04,850] [INFO] Task started: Prodigal
[2024-01-24 14:50:04,850] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4cf5fc9-6c97-4da7-b308-427f77098413/GCF_009758205.1_ASM975820v1_genomic.fna.gz | prodigal -d GCF_009758205.1_ASM975820v1_genomic.fna/cds.fna -a GCF_009758205.1_ASM975820v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:50:39,527] [INFO] Task succeeded: Prodigal
[2024-01-24 14:50:39,528] [INFO] Task started: HMMsearch
[2024-01-24 14:50:39,528] [INFO] Running command: hmmsearch --tblout GCF_009758205.1_ASM975820v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5343bc1a-74c8-4481-971c-c0df48e5432d/dqc_reference/reference_markers.hmm GCF_009758205.1_ASM975820v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:50:39,844] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:50:39,845] [INFO] Found 6/6 markers.
[2024-01-24 14:50:39,905] [INFO] Query marker FASTA was written to GCF_009758205.1_ASM975820v1_genomic.fna/markers.fasta
[2024-01-24 14:50:39,905] [INFO] Task started: Blastn
[2024-01-24 14:50:39,906] [INFO] Running command: blastn -query GCF_009758205.1_ASM975820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5343bc1a-74c8-4481-971c-c0df48e5432d/dqc_reference/reference_markers.fasta -out GCF_009758205.1_ASM975820v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:40,474] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:40,477] [INFO] Selected 13 target genomes.
[2024-01-24 14:50:40,478] [INFO] Target genome list was writen to GCF_009758205.1_ASM975820v1_genomic.fna/target_genomes.txt
[2024-01-24 14:50:40,487] [INFO] Task started: fastANI
[2024-01-24 14:50:40,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4cf5fc9-6c97-4da7-b308-427f77098413/GCF_009758205.1_ASM975820v1_genomic.fna.gz --refList GCF_009758205.1_ASM975820v1_genomic.fna/target_genomes.txt --output GCF_009758205.1_ASM975820v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:51:01,071] [INFO] Task succeeded: fastANI
[2024-01-24 14:51:01,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5343bc1a-74c8-4481-971c-c0df48e5432d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:51:01,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5343bc1a-74c8-4481-971c-c0df48e5432d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:51:01,081] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:51:01,082] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:51:01,082] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Chitinophaga tropicalis	strain=ysch24	GCA_009758205.1	2683588	2683588	type	True	100.0	2628	2630	95	conclusive
Chitinophaga filiformis	strain=DSM 527	GCA_900102545.1	104663	104663	type	True	79.7509	1025	2630	95	below_threshold
Chitinophaga ginsengisoli	strain=DSM 18107	GCA_003014595.1	363837	363837	type	True	79.7127	999	2630	95	below_threshold
Chitinophaga pinensis	strain=DSM 2588	GCA_000024005.1	79329	79329	type	True	79.5553	842	2630	95	below_threshold
Chitinophaga agri	strain=H33E-04	GCA_010093065.1	2703787	2703787	type	True	79.3671	784	2630	95	below_threshold
Chitinophaga rhizophila	strain=B61	GCA_019492185.1	2866212	2866212	type	True	79.2769	754	2630	95	below_threshold
Chitinophaga oryziterrae	strain=JCM 16595	GCA_009758125.1	1031224	1031224	type	True	78.9045	726	2630	95	below_threshold
Chitinophaga sancti	strain=DSM 784	GCA_900119105.1	1004	1004	type	True	78.6397	602	2630	95	below_threshold
Chitinophaga silvisoli	strain=K20C18050901	GCA_003412465.1	2291814	2291814	type	True	78.6024	627	2630	95	below_threshold
Chitinophaga rupis	strain=DSM 21039	GCA_900109685.1	573321	573321	type	True	77.7271	506	2630	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	75.731	86	2630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:51:01,092] [INFO] DFAST Taxonomy check result was written to GCF_009758205.1_ASM975820v1_genomic.fna/tc_result.tsv
[2024-01-24 14:51:01,093] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:51:01,093] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:51:01,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5343bc1a-74c8-4481-971c-c0df48e5432d/dqc_reference/checkm_data
[2024-01-24 14:51:01,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:51:01,170] [INFO] Task started: CheckM
[2024-01-24 14:51:01,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009758205.1_ASM975820v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009758205.1_ASM975820v1_genomic.fna/checkm_input GCF_009758205.1_ASM975820v1_genomic.fna/checkm_result
[2024-01-24 14:52:33,078] [INFO] Task succeeded: CheckM
[2024-01-24 14:52:33,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:52:33,100] [INFO] ===== Completeness check finished =====
[2024-01-24 14:52:33,100] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:52:33,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009758205.1_ASM975820v1_genomic.fna/markers.fasta)
[2024-01-24 14:52:33,101] [INFO] Task started: Blastn
[2024-01-24 14:52:33,101] [INFO] Running command: blastn -query GCF_009758205.1_ASM975820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5343bc1a-74c8-4481-971c-c0df48e5432d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009758205.1_ASM975820v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:52:33,882] [INFO] Task succeeded: Blastn
[2024-01-24 14:52:33,885] [INFO] Selected 13 target genomes.
[2024-01-24 14:52:33,885] [INFO] Target genome list was writen to GCF_009758205.1_ASM975820v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:52:33,949] [INFO] Task started: fastANI
[2024-01-24 14:52:33,949] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4cf5fc9-6c97-4da7-b308-427f77098413/GCF_009758205.1_ASM975820v1_genomic.fna.gz --refList GCF_009758205.1_ASM975820v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009758205.1_ASM975820v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:52:53,579] [INFO] Task succeeded: fastANI
[2024-01-24 14:52:53,589] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:52:53,590] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_009758205.1	s__Chitinophaga sp009758205	100.0	2628	2630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016467415.1	s__Chitinophaga sp016467415	79.8183	995	2630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102545.1	s__Chitinophaga filiformis	79.761	1023	2630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014595.1	s__Chitinophaga ginsengisoli	79.7177	998	2630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182155.1	s__Chitinophaga sp003182155	79.6985	872	2630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142925.1	s__Chitinophaga sp900142925	79.6553	1037	2630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168105.1	s__Chitinophaga sp902168105	79.6408	855	2630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024005.1	s__Chitinophaga pinensis	79.5553	842	2630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114995.1	s__Chitinophaga sp900114995	79.5286	867	2630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009758125.1	s__Chitinophaga oryziterrae	78.9108	724	2630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110995.1	s__Chitinophaga sp900110995	78.8967	739	2630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119105.1	s__Chitinophaga sancti	78.6327	603	2630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003412465.1	s__Chitinophaga silvisoli	78.6007	627	2630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:52:53,591] [INFO] GTDB search result was written to GCF_009758205.1_ASM975820v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:52:53,592] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:52:53,595] [INFO] DFAST_QC result json was written to GCF_009758205.1_ASM975820v1_genomic.fna/dqc_result.json
[2024-01-24 14:52:53,596] [INFO] DFAST_QC completed!
[2024-01-24 14:52:53,596] [INFO] Total running time: 0h2m50s